PDBsum entry 1n3i

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Transferase PDB id
Protein chains
262 a.a. *
PO4 ×3
DIH ×3
Waters ×432
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of mycobacterium tuberculosis pnp with transition state analog dadme-immh
Structure: Purine nucleoside phosphorylase. Chain: a, b, c. Synonym: pnp. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Trimer (from PQS)
1.90Å     R-factor:   0.183     R-free:   0.213
Authors: A.Lewandowicz,W.Shi,G.B.Evans,P.C.Tyler,R.H.Furneaux, L.A.Basso,D.S.Santos,S.C.Almo,V.L.Schramm
Key ref:
A.Lewandowicz et al. (2003). Over-the-barrier transition state analogues and crystal structure with Mycobacterium tuberculosis purine nucleoside phosphorylase. Biochemistry, 42, 6057-6066. PubMed id: 12755607 DOI: 10.1021/bi0343830
28-Oct-02     Release date:   30-Sep-03    
Go to PROCHECK summary

Protein chains
P9WP00  (PUNA_MYCTO) -  Purine nucleoside phosphorylase
268 a.a.
262 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Purine-nucleoside phosphorylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
1. Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate
2. Purine deoxynucleoside + phosphate = purine + 2'-deoxy-alpha-D-ribose 1-phosphate
Purine nucleoside
Bound ligand (Het Group name = DIH)
matches with 48.00% similarity
Bound ligand (Het Group name = PO4)
corresponds exactly
= purine
+ alpha-D-ribose 1-phosphate
Purine deoxynucleoside
+ phosphate
= purine
+ 2'-deoxy-alpha-D-ribose 1-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nucleobase-containing compound metabolic process   2 terms 
  Biochemical function     catalytic activity     5 terms  


DOI no: 10.1021/bi0343830 Biochemistry 42:6057-6066 (2003)
PubMed id: 12755607  
Over-the-barrier transition state analogues and crystal structure with Mycobacterium tuberculosis purine nucleoside phosphorylase.
A.Lewandowicz, W.Shi, G.B.Evans, P.C.Tyler, R.H.Furneaux, L.A.Basso, D.S.Santos, S.C.Almo, V.L.Schramm.
Stable chemical analogues of enzymatic transition states are imperfect mimics since they lack the partial bond character of the transition state. We synthesized structural variants of the Immucillins as transition state analogues for purine nucleoside phosphorylase and characterized them with the enzyme from Mycobacterium tuberculosis (MtPNP). PNPs form transition states with ribooxacarbenium ion character and catalyze nucleophilic displacement reactions by migration of the cationic ribooxacarbenium carbon between the enzymatically immobilized purine and phosphate nucleophiles. As bond-breaking progresses, carbocation character builds on the ribosyl group, the distance between the purine and the carbocation increases, and the distance between carbocation and phosphate anion decreases. Transition state analogues were produced with carbocation character and increased distance between the ribooxacarbenium ion and the purine mimics by incorporating a methylene bridge between these groups. Immucillin-H (ImmH), DADMe-ImmH, and DADMe-ImmG mimic the transition state of MtPNP and are slow-onset, tight-binding inhibitors of MtPNP with equilibrium dissociation constants of 650, 42, and 24 pM. Crystal structures of MtPNP complexes with ImmH and DADMe-ImmH reveal an ion-pair between the inhibitor cation and the nucleophilic phosphoryl anion. The stronger ion-pair (2.7 A) is found with DADMe-ImmH. The position of bound ImmH resembles the substrate side of the transition state barrier, and DADMe-ImmH more closely resembles the product side of the barrier. The ability to probe both substrate and product sides of the transition state barrier provides expanded opportunities to explore transition state analogue design in N-ribosyltransferases. This approach has resulted in the highest affinity transition state analogues known for MtPNP.

Literature references that cite this PDB file's key reference

  PubMed id Reference
20170081 H.Deng, R.Callender, V.L.Schramm, and C.Grubmeyer (2010).
Pyrophosphate activation in hypoxanthine--guanine phosphoribosyltransferase with transition state analogue.
  Biochemistry, 49, 2705-2714.  
19778725 M.Ghanem, A.S.Murkin, and V.L.Schramm (2009).
Ribocation transition state capture and rebound in human purine nucleoside phosphorylase.
  Chem Biol, 16, 971-979.  
19191546 M.Ghanem, N.Zhadin, R.Callender, and V.L.Schramm (2009).
Loop-tryptophan human purine nucleoside phosphorylase reveals submillisecond protein dynamics.
  Biochemistry, 48, 3658-3668.  
18234834 S.Saen-Oon, M.Ghanem, V.L.Schramm, and S.D.Schwartz (2008).
Remote mutations and active site dynamics correlate with catalytic properties of purine nucleoside phosphorylase.
  Biophys J, 94, 4078-4088.  
17407325 A.S.Murkin, M.R.Birck, A.Rinaldo-Matthis, W.Shi, E.A.Taylor, S.C.Almo, and V.L.Schramm (2007).
Neighboring group participation in the transition state of human purine nucleoside phosphorylase.
  Biochemistry, 46, 5038-5049.
PDB codes: 2a0w 2a0x 2a0y 2oc4 2oc9 2on6
15746096 J.E.Lee, V.Singh, G.B.Evans, P.C.Tyler, R.H.Furneaux, K.A.Cornell, M.K.Riscoe, V.L.Schramm, and P.L.Howell (2005).
Structural rationale for the affinity of pico- and femtomolar transition state analogues of Escherichia coli 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.
  J Biol Chem, 280, 18274-18282.
PDB codes: 1y6q 1y6r
15983408 W.Bu, E.C.Settembre, M.H.el Kouni, and S.E.Ealick (2005).
Structural basis for inhibition of Escherichia coli uridine phosphorylase by 5-substituted acyclouridines.
  Acta Crystallogr D Biol Crystallogr, 61, 863-872.
PDB codes: 1u1c 1u1d 1u1e 1u1f 1u1g
12842889 A.Lewandowicz, P.C.Tyler, G.B.Evans, R.H.Furneaux, and V.L.Schramm (2003).
Achieving the ultimate physiological goal in transition state analogue inhibitors for purine nucleoside phosphorylase.
  J Biol Chem, 278, 31465-31468.  
12915092 M.Bellinzoni, and G.Riccardi (2003).
Techniques and applications: The heterologous expression of Mycobacterium tuberculosis genes is an uphill road.
  Trends Microbiol, 11, 351-358.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.